The Knowledge Engineering Review
A Resourceomic Grid for bioinformatics
Future Generation Computer Systems
Engineering agent-mediated integration of bioinformatics analysis tools
Multiagent and Grid Systems - Multi-agent systems for medicine, computational biology, and bioinformatics
A framework for the definition of metamodels for Computer-Aided Software Engineering tools
Information and Software Technology
Workflow-driven tool integration using model transformations
Graph transformations and model-driven engineering
Enacting proactive workflows engine in e-science
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part III
WWW information integration oriented classification ontology integrating approach
KSEM'06 Proceedings of the First international conference on Knowledge Science, Engineering and Management
An agent-oriented conceptual framework for systems biology
Transactions on Computational Systems Biology III
Hermes: agent-based middleware for mobile computing
SFM-Moby'05 Proceedings of the 5th international conference on Formal Methods for the Design of Computer, Communication, and Software Systems: mobile computing
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Tool integration is a very difficult challenge. Problems may arise at different abstraction levels and from several sources such as heterogeneity of manipulated data, incompatible interfaces, or uncoordinated services, to name just a few examples. On the other hand, applications based on the coherent composition of activities, components, services, and data from heterogeneous sources are increasingly present in our everyday lives. Consequently, tool integration takes on increasing significance. In this paper we analyze the tool-integration problem at different abstraction levels and discuss different views on a layered software architecture that we have designed specifically for a middleware that supports the execution of distributed applications for the orchestration of human/system activities. We noticed that the agent paradigm provided a suitable technology for abstraction in tool integration. Throughout the paper, the discussion refers to a case study in the bioinformatics domain.